title: Evaluation of a high-throughput, microfluidics platform for performing TaqMan™ qPCR using formalin-fixed paraffin-embedded tumors.
abstract: BACKGROUND
  Compared with the standard qPCR, nanoliter-scale qPCR can use smaller quantities of RNA and increase throughput. The TaqMan™ OpenArray® NT Cycler System was assessed for use with degraded RNA from formalin-fixed paraffin-embedded (FFPE) tumors.
  
  
  RESULTS
  Expression of candidate prognostic genes was quantified using the OpenArray platform and matching fresh frozen and FFPE patient renal cell carcinomas. Reverse transcription, with gene-specific reverse transcription and preamplification, optimized the percentage of detectable transcripts. When using high quality RNA from fresh frozen tumors, the OpenArray platform identified 30 prognostic genes. However, when using RNA from FFPE tumors, only 13 prognostic genes were identified, but this increased to 33 with addition of preamplification.
  
  
  CONCLUSIONS
  The OpenArray platform can be optimized to quantify gene expressions from FFPE tumors.
authors.affiliation: Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
authors.forename: Ping
authors.initials: P
authors.lastname: Li
authors.forename: Elena
authors.initials: E
authors.lastname: Grigorenko
authors.forename: Vince
authors.initials: V
authors.lastname: Funari
authors.forename: Edward
authors.initials: E
authors.lastname: Enright
authors.forename: Hao
authors.initials: H
authors.lastname: Zhang
authors.forename: Hyung L
authors.initials: HL
authors.lastname: Kim
mesh_terms: D002292:Carcinoma, Renal Cell / Q000235:genetics* / Q000473:pathology; D005557:Formaldehyde; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D007680:Kidney Neoplasms / Q000235:genetics* / Q000473:pathology; D044085:Microfluidics / Q000379:methods*; D016612:Paraffin Embedding; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*
chemical_list: D005557:Formaldehyde